1
|
Gyimesi G, Hediger MA. Systematic in silico discovery of novel solute carrier-like proteins from proteomes. PLoS One 2022; 17:e0271062. [PMID: 35901096 PMCID: PMC9333335 DOI: 10.1371/journal.pone.0271062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 06/22/2022] [Indexed: 12/26/2022] Open
Abstract
Solute carrier (SLC) proteins represent the largest superfamily of transmembrane transporters. While many of them play key biological roles, their systematic analysis has been hampered by their functional and structural heterogeneity. Based on available nomenclature systems, we hypothesized that many as yet unidentified SLC transporters exist in the human genome, which await further systematic analysis. Here, we present criteria for defining "SLC-likeness" to curate a set of "SLC-like" protein families from the Transporter Classification Database (TCDB) and Protein families (Pfam) databases. Computational sequence similarity searches surprisingly identified ~120 more proteins in human with potential SLC-like properties compared to previous annotations. Interestingly, several of these have documented transport activity in the scientific literature. To complete the overview of the "SLC-ome", we present an algorithm to classify SLC-like proteins into protein families, investigating their known functions and evolutionary relationships to similar proteins from 6 other clinically relevant experimental organisms, and pinpoint structural orphans. We envision that our work will serve as a stepping stone for future studies of the biological function and the identification of the natural substrates of the many under-explored SLC transporters, as well as for the development of new therapeutic applications, including strategies for personalized medicine and drug delivery.
Collapse
Affiliation(s)
- Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department for BioMedical Research, Inselspital, University of Bern, Bern, Switzerland
- * E-mail: (GG); (MAH)
| | - Matthias A. Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department for BioMedical Research, Inselspital, University of Bern, Bern, Switzerland
- * E-mail: (GG); (MAH)
| |
Collapse
|
2
|
Bouchard-Mercier A, de Toro-Martín J, Nadeau M, Lescelleur O, Lebel S, Richard D, Biertho L, Tchernof A, Vohl MC. Molecular remodeling of adipose tissue is associated with metabolic recovery after weight loss surgery. Lab Invest 2022; 20:283. [PMID: 35739539 PMCID: PMC9219157 DOI: 10.1186/s12967-022-03485-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/13/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND Bariatric surgery is an effective therapy for individuals with severe obesity to achieve sustainable weight loss and to reduce comorbidities. Examining the molecular signature of subcutaneous adipose tissue (SAT) following different types of bariatric surgery may help in gaining further insight into their distinct metabolic impact. RESULTS Subjects undergoing biliopancreatic diversion with duodenal switch (BPD-DS) showed a significantly higher percentage of total weight loss than those undergoing gastric bypass or sleeve gastrectomy (RYGB + SG) (41.7 ± 4.6 vs 28.2 ± 6.8%; p = 0.00005). Individuals losing more weight were also significantly more prone to achieve both type 2 diabetes and dyslipidemia remission (OR = 0.75; 95%CI = 0.51-0.91; p = 0.03). Whole transcriptome and methylome profiling showed that bariatric surgery induced a profound molecular remodeling of SAT at 12 months postoperative, mainly through gene down-regulation and hypermethylation. The extent of changes observed was greater following BPD-DS, with 61.1% and 49.8% of up- and down-regulated genes, as well as 85.7% and 70.4% of hyper- and hypomethylated genes being exclusive to this procedure, and mostly associated with a marked decrease of immune and inflammatory responses. Weight loss was strongly associated with genes being simultaneously differentially expressed and methylated in BPD-DS, with the strongest association being observed for GPD1L (r2 = 0.83; p = 1.4 × 10-6). CONCLUSIONS Present findings point to the greater SAT molecular remodeling following BPD-DS as potentially linked with higher metabolic remission rates. These results will contribute to a better understanding of the metabolic pathways involved in the response to bariatric surgery and will eventually lead to the development of gene targets for the treatment of obesity. Trial registration ClinicalTrials.gov NCT02390973.
Collapse
Affiliation(s)
- Annie Bouchard-Mercier
- School of Nutrition and Centre Nutrition, Santé et Société (NUTRISS)-Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Pavillon des Services (suite 2729K), 2440 Hochelaga Blvd, Quebec City, QC, G1V 0A6, Canada
| | - Juan de Toro-Martín
- School of Nutrition and Centre Nutrition, Santé et Société (NUTRISS)-Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Pavillon des Services (suite 2729K), 2440 Hochelaga Blvd, Quebec City, QC, G1V 0A6, Canada
| | - Mélanie Nadeau
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), 2725 chemin Sainte-Foy, Quebec City, QC, G1V 4G5, Canada
| | - Odette Lescelleur
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), 2725 chemin Sainte-Foy, Quebec City, QC, G1V 4G5, Canada
| | - Stéfane Lebel
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), 2725 chemin Sainte-Foy, Quebec City, QC, G1V 4G5, Canada
| | - Denis Richard
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), 2725 chemin Sainte-Foy, Quebec City, QC, G1V 4G5, Canada
| | - Laurent Biertho
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), 2725 chemin Sainte-Foy, Quebec City, QC, G1V 4G5, Canada
| | - André Tchernof
- Centre de recherche de l'institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), 2725 chemin Sainte-Foy, Quebec City, QC, G1V 4G5, Canada
| | - Marie-Claude Vohl
- School of Nutrition and Centre Nutrition, Santé et Société (NUTRISS)-Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Pavillon des Services (suite 2729K), 2440 Hochelaga Blvd, Quebec City, QC, G1V 0A6, Canada.
| |
Collapse
|
3
|
Izquierdo AG, Carreira MC, Boughanem H, Moreno-Navarrete JM, Nicoletti CF, Oliver P, de Luis D, Nonino CB, Portillo MP, Martinez-Olmos MA, Fernandez-Real JM, Tinahones FJ, Martinez JA, Macias-González M, Casanueva FF, Crujeiras AB. Adipose tissue and blood leukocytes ACE2 DNA methylation in obesity and after weight loss. Eur J Clin Invest 2022; 52:e13685. [PMID: 34582564 DOI: 10.1111/eci.13685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/26/2021] [Accepted: 09/21/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Obesity was consistently associated with a poor prognosis in patients with COVID-19. Epigenetic mechanisms were proposed as the link between obesity and comorbidities risk. AIM To evaluate the methylation levels of angiotensin-converting enzyme 2 (ACE2) gene, the main entry receptor of SARS-CoV-2, in different depots of adipose tissue (AT) and leukocytes (PBMCs) in obesity and after weight loss therapy based on a very-low-calorie ketogenic diet (VLCKD), a balanced hypocaloric diet (HCD) or bariatric surgery (BS). MATERIALS AND METHODS DNA methylation levels of ACE2 were extracted from our data sets generated by the hybridization of subcutaneous (SAT) (n = 32) or visceral (VAT; n = 32) adipose tissue, and PBMCs (n = 34) samples in Infinium HumanMethylation450 BeadChips. Data were compared based on the degree of obesity and after 4-6 months of weight loss either by following a nutritional or surgical treatment and correlated with ACE2 transcript levels. RESULTS As compared with normal weight, VAT from patients with obesity showed higher ACE2 methylation levels. These differences were mirrored in PBMCs but not in SAT. The observed obesity-associated methylation of ACE2 was reversed after VLCKD and HCD but not after BS. Among the studied CpG sites, cg16734967 and cg21598868, located at the promoter, were the most affected and correlated with BMI. The observed DNA methylation pattern was inversely correlated with ACE2 expression. CONCLUSION Obesity-related VAT shows hypermethylation and downregulation of the ACE2 gene that is mirrored in PBMCs and is restored after nutritional weight reduction therapy. The results warrant the necessity to further evaluate its implication for COVID-19 pathogenesis.
Collapse
Affiliation(s)
- Andrea G Izquierdo
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain.,Endocrine Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain.,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Marcos C Carreira
- Endocrine Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain.,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Molecular Endocrinology Group, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain
| | - Hatim Boughanem
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), Malaga, Spain
| | - Jose M Moreno-Navarrete
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi) and Universitat de Girona, Girona, Spain
| | - Carolina F Nicoletti
- Department of Internal Medicine, Laboratory of Nutrigenomic Studies, Ribeirao Preto Medical School (FMRP) University of Sao Paulo (USP), Sao Paulo, Brazil
| | - Paula Oliver
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Nutrigenomics and Obesity Group, University of the Balearic Islands and Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
| | - Daniel de Luis
- Center of Investigation of Endocrinology and Nutrition, Medicine School and Department of Endocrinology and Investigation, Hospital Clinico Universitario, University of Valladolid, Valladolid, Spain
| | - Carla B Nonino
- Department of Internal Medicine, Laboratory of Nutrigenomic Studies, Ribeirao Preto Medical School (FMRP) University of Sao Paulo (USP), Sao Paulo, Brazil
| | - Maria P Portillo
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Nutrition and Obesity Group, Department of Nutrition and Food Science, Lucio Lascaray Research Institute and Bioaraba Health Research Institute, University of the Basque Country (UPV/EHU), Vitoria, Spain
| | - Miguel A Martinez-Olmos
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain.,Endocrine Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain.,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Jose M Fernandez-Real
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi) and Universitat de Girona, Girona, Spain
| | - Francisco J Tinahones
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), Malaga, Spain
| | - J Alfredo Martinez
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Department of Nutrition, Food Science and Physiology, Centre for Nutrition Research, Navarra Institute for Health Research, University of Navarra (UNAV) and IdiSNA, Pamplona, Spain.,Nutritional Genomics and Epigenomics Group, IMDEA Food, CEI UAM + CSIC, Madrid, Spain
| | - Manuel Macias-González
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA), Malaga, Spain
| | - Felipe F Casanueva
- Endocrine Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain.,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.,Molecular Endocrinology Group, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain.,Endocrine Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain.,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| |
Collapse
|
4
|
Porca C, Rodriguez-Carnero G, Tejera C, Andujar P, Casanueva FF, Crujeiras AB, Bellido D. Effectiveness to promote weight loss maintenance and healthy lifestyle habits of a group educational intervention program in adults with obesity: IGOBE program. Obes Res Clin Pract 2021; 15:570-578. [PMID: 34742669 DOI: 10.1016/j.orcp.2021.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND To achieve sustainable weight loss and healthy lifestyle changes is a huge challenge in the fight against obesity. The objective of this study was to evaluate the effectiveness to promote weight loss maintenance and healthy lifestyle habits of a group educational intervention program, Group Intervention in OBEsity (IGOBE), compared with a usual care therapy to lose weight. METHODS Patients with obesity (n = 437; 18.5% men, 18-77 years and 40.4 ± 6.7 kg/m2) were randomised into two groups to follow a prospective interventional real-life study: a control group (CG), treated with usual clinical practice, and an intervention group (IG), in which the patients participate in a group intervention program on healthy lifestyle habits with weekly sessions for six weeks, after which a re-evaluation was made at six months and at 12 months of follow-up. After finishing the study dropout rates were 44.6% in CG and 43.4% in IG. Anthropometric, dietetic habits and body composition data were analysed in both groups at the pre-intervention and post-interventions of the subjects by completer's analysis. RESULTS At 12 months of following IGOBE program, the IG achieved greater weight loss (-7.1% of the initial weight) than the CG, which exhibited a weight gain (3.0% of the initial weight). The body weight change induced in the IG was accompanied by a reduction in fat mass, particularly visceral fat and waist circumference. Relevantly, the IG adhered to a healthy dietary pattern and changed its eating habits, which correlated with the improvement in body weight. CONCLUSIONS Intensive educational group treatment that induces a change of eating habits and adherence to healthy dietary pattern is more effective in a long-term to counteract obesity traits than a standard treatment performed individually. The IGOBE program could be a cost-effective practice in the clinical management of obesity.
Collapse
Affiliation(s)
- Cristina Porca
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Univeristario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain; Division of Endocrinology, Complejo Hospitalario Universitario de Ferrol (CHUF/SERGAS) and Coruña University, Ferrol, Spain
| | - Gemma Rodriguez-Carnero
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Univeristario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain; Division of Endocrinology and Nutrition, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Cristina Tejera
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Univeristario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain; Division of Endocrinology, Complejo Hospitalario Universitario de Ferrol (CHUF/SERGAS) and Coruña University, Ferrol, Spain
| | - Paula Andujar
- Division of Endocrinology, Complejo Hospitalario Universitario de Ferrol (CHUF/SERGAS) and Coruña University, Ferrol, Spain
| | - Felipe F Casanueva
- Division of Endocrinology and Nutrition, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain; Molecular Endocrinology Group, Instituto de Investigacion Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain; Centro de Investigacion Biomedica en Red Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Univeristario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain; Centro de Investigacion Biomedica en Red Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.
| | - Diego Bellido
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Univeristario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain; Division of Endocrinology, Complejo Hospitalario Universitario de Ferrol (CHUF/SERGAS) and Coruña University, Ferrol, Spain.
| |
Collapse
|
5
|
Izquierdo AG, Boughanem H, Diaz-Lagares A, Arranz-Salas I, Esteller M, Tinahones FJ, Casanueva FF, Macias-Gonzalez M, Crujeiras AB. DNA methylome in visceral adipose tissue can discriminate patients with and without colorectal cancer. Epigenetics 2021; 17:665-676. [PMID: 34311674 DOI: 10.1080/15592294.2021.1950991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Adipose tissue dysfunction, particularly the visceral (VAT) compartment, has been proposed to play a relevant role in colorectal cancer (CRC) development and progression. Epigenetic mechanisms could be involved in this association. The current study aimed to evaluate if specific epigenetic marks in VAT are associated with colorectal cancer (CRC) to identify epigenetic hallmarks of adipose tissue-related CRC. Epigenome-wide DNA methylation was evaluated in VAT from 25 healthy participants and 29 CRC patients, using the Infinium HumanMethylation450K BeadChip. The epigenome-wide methylation analysis identified 170,184 sites able to perfectly separate the CRC and healthy samples. The differentially methylated CpG sites (DMCpGs) showed a global trend for increased methylated levels in CRC with respect to healthy group. Most of the genes encoded by the DMCpGs belonged to metabolic pathways and cell cycle, insulin resistance, and adipocytokine signalling, as well as tumoural transformation processes. In gene-specific analyses, involved genes biologically relevant for the development of CRC include PTPRN2, MAD1L1, TNXB, DIP2C, INPP5A, HDCA4, PRDM16, RPTOR, ATP11A, TBCD, PABPC3, and IER2. The methylation level of some of them showed a discriminatory capacity for detecting CRC higher than 90%, showing IER2 to have the highest capacity. This study reveals that a specific methylation pattern of VAT is associated with CRC. Some of the epigenetic marks identified could provide useful tools for the prediction and personalized treatment of CRC connected to excess adiposity.
Collapse
Affiliation(s)
- Andrea G Izquierdo
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto De Investigacion Sanitaria De Santiago De Compostela (IDIS), Complejo Hospitalario Universitario De Santiago De Compostela (CHUS/SERGAS), and Centro De Investigacion Biomedica En Red Fisiopatologia De La Obesidad Y Nutricion (Ciberobn), Spain
| | - Hatim Boughanem
- Department of Endocrinology and Nutrition, Virgen De La Victoria University Hospital, University of Malaga (IBIMA), Spain and Centro De Investigacion Biomedica En Red Physiopathology of Obesity and Nutrition (Ciberobn), Málaga, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenetics, Translational Medical Oncology (Oncomet), Instituto De Investigacion Sanitaria De Santiago De Compostela (IDIS), Complejo Hospitalario Universitario De Santiago De Compostela (CHUS/SERGAS), and Centro De Investigacion Biomedica En Red Oncología (CIBERONC), Spain
| | - Isabel Arranz-Salas
- Unit of Anatomical Pathology, Virgen de la Victoria University Hospital, Málaga, Spain
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain; Centro De Investigacion Biomedica En Red Oncologia (CIBERONC), Madrid, Spain; Institucio Catalana De Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Francisco J Tinahones
- Department of Endocrinology and Nutrition, Virgen De La Victoria University Hospital, University of Malaga (IBIMA), Spain and Centro De Investigacion Biomedica En Red Physiopathology of Obesity and Nutrition (Ciberobn), Málaga, Spain
| | - Felipe F Casanueva
- Molecular and Cellular Endocrinology Group. Instituto De Investigacion Sanitaria De Santiago De Compostela (IDIS), Complejo Hospitalario Universitario De Santiago De Compostela (CHUS), Santiago De Compostela University (USC) and Centro De Investigacion Biomedica En Red Fisiopatologia De La Obesidad Y Nutricion (Ciberobn), Spain
| | - Manuel Macias-Gonzalez
- Department of Endocrinology and Nutrition, Virgen De La Victoria University Hospital, University of Malaga (IBIMA), Spain and Centro De Investigacion Biomedica En Red Physiopathology of Obesity and Nutrition (Ciberobn), Málaga, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto De Investigacion Sanitaria De Santiago De Compostela (IDIS), Complejo Hospitalario Universitario De Santiago De Compostela (CHUS/SERGAS), and Centro De Investigacion Biomedica En Red Fisiopatologia De La Obesidad Y Nutricion (Ciberobn), Spain
| |
Collapse
|
6
|
Xu Y, Chen X, Yu L, Wang Y, Wang H, Wu Z, Wu S, Bao W. SLC4A11 and MFSD3 Gene Expression Changes in Deoxynivalenol Treated IPEC-J2 Cells. Front Genet 2021; 12:697883. [PMID: 34367255 PMCID: PMC8335166 DOI: 10.3389/fgene.2021.697883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Deoxynivalenol (DON) caused serious cytotoxicity for animal cells. However, genes involved in regulating DON toxicity and the underlying molecular mechanisms remain largely unknown. This study explored the role of SLC4A11 and MFSD3 in alleviating DON toxicity and analyzed the DNA methylation changes of these two genes. Viability and cell cycle analysis showed that DON exposure decreased the IPEC-J2 viability (P < 0.01), blocked the cell cycle in the G2/M phase (P < 0.01), and increased the rate of apoptosis (P < 0.05). Expression of the SLC4A11 and MFSD3 genes was significantly downregulated upon DON exposure (P < 0.01). Overexpression of SLC4A11 and MFSD3 can enhance the cell viability (P < 0.01). DNA methylation assays indicated that promoter methylation of SLC4A11 (mC-1 and mC-23) and MFSD3 (mC-1 and mC-12) were significantly higher compared with those in the controls and correlated negatively with mRNA expression (P < 0.05). Further analysis showed that mC-1 of SLC4A11 and MFSD3 was located in transcription factor binding sites for NF-1 and Sp1. Our findings revealed the novel biological functions of porcine SLC4A11 and MFSD3 genes in regulating the cytotoxic effects induced by DON, and may contribute to the detection of biomarkers and drug targets for predicting and eliminating the potential toxicity of DON.
Collapse
Affiliation(s)
- Yafei Xu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaolei Chen
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Luchen Yu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yi Wang
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Haifei Wang
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhengchang Wu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shenglong Wu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| |
Collapse
|
7
|
Crujeiras AB, Izquierdo AG, Primo D, Milagro FI, Sajoux I, Jácome A, Fernandez-Quintela A, Portillo MP, Martínez JA, Martinez-Olmos MA, de Luis D, Casanueva FF. Epigenetic landscape in blood leukocytes following ketosis and weight loss induced by a very low calorie ketogenic diet (VLCKD) in patients with obesity. Clin Nutr 2021; 40:3959-3972. [PMID: 34139469 DOI: 10.1016/j.clnu.2021.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND The molecular mechanisms underlying the potential health benefits of a ketogenic diet are unknown and could be mediated by epigenetic mechanisms. OBJECTIVE To identify the changes in the obesity-related methylome that are mediated by the induced weight loss or are dependent on ketosis in subjects with obesity underwent a very-low calorie ketogenic diet (VLCKD). METHODS Twenty-one patients with obesity (n = 12 women, 47.9 ± 1.02 yr, 33.0 ± 0.2 kg/m2) after 6 months on a VLCKD and 12 normal weight volunteers (n = 6 women, 50.3 ± 6.2 yrs, 22.7 ± 1.5 kg/m2) were studied. Data from the Infinium MethylationEPIC BeadChip methylomes of blood leukocytes were obtained at time points of ketotic phases (basal, maximum ketosis, and out of ketosis) during VLCKD (n = 10) and at baseline in volunteers (n = 12). Results were further validated by pyrosequencing in representative cohort of patients on a VLCKD (n = 18) and correlated with gene expression. RESULTS After weight reduction by VLCKD, differences were found at 988 CpG sites (786 unique genes). The VLCKD altered methylation levels in patients with obesity had high resemblance with those from normal weight volunteers and was concomitant with a downregulation of DNA methyltransferases (DNMT)1, 3a and 3b. Most of the encoded genes were involved in metabolic processes, protein metabolism, and muscle, organ, and skeletal system development. Novel genes representing the top scoring associated events were identified, including ZNF331, FGFRL1 (VLCKD-induced weight loss) and CBFA2T3, C3orf38, JSRP1, and LRFN4 (VLCKD-induced ketosis). Interestingly, ZNF331 and FGFRL1 were validated in an independent cohort and inversely correlated with gene expression. CONCLUSIONS The beneficial effects of VLCKD therapy on obesity involve a methylome more suggestive of normal weight that could be mainly mediated by the VLCKD-induced ketosis rather than weight loss.
Collapse
Affiliation(s)
- Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Spain; CIBER Fisiopatologia de La Obesidad y Nutricion (CIBERobn), Spain.
| | - Andrea G Izquierdo
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Spain; CIBER Fisiopatologia de La Obesidad y Nutricion (CIBERobn), Spain
| | - David Primo
- Center of Investigation of Endocrinology and Nutrition, Medicine School and Department of Endocrinology and Investigation, Hospital Clinico Universitario, University of Valladolid, Valladolid, Spain
| | - Fermin I Milagro
- Department of Nutrition, Food Science and Physiology, Centre for Nutrition Research, University of Navarra (UNAV) and IdiSNA, Navarra Institute for Health Research, 31009, Pamplona, Spain; CIBER Fisiopatologia de La Obesidad y Nutricion (CIBERobn), Spain
| | - Ignacio Sajoux
- Medical Department Pronokal Group, PronokalGroup, Barcelona, Spain
| | - Amalia Jácome
- Department of Mathematics, MODES Group, CITIC, Universidade da Coruña, Faculty of Science, A Coruña, Spain
| | - Alfredo Fernandez-Quintela
- Nutrition and Obesity Group, Department of Nutrition and Food Science, University of the Basque Country (UPV/EHU), Lucio Lascaray Research Institute and Health Research Institute BIOARABA, Vitoria, Spain; CIBER Fisiopatologia de La Obesidad y Nutricion (CIBERobn), Spain
| | - María P Portillo
- Nutrition and Obesity Group, Department of Nutrition and Food Science, University of the Basque Country (UPV/EHU), Lucio Lascaray Research Institute and Health Research Institute BIOARABA, Vitoria, Spain; CIBER Fisiopatologia de La Obesidad y Nutricion (CIBERobn), Spain
| | - J Alfredo Martínez
- Department of Nutrition, Food Science and Physiology, Centre for Nutrition Research, University of Navarra (UNAV) and IdiSNA, Navarra Institute for Health Research, 31009, Pamplona, Spain; CIBER Fisiopatologia de La Obesidad y Nutricion (CIBERobn), Spain
| | - Miguel A Martinez-Olmos
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Spain; CIBER Fisiopatologia de La Obesidad y Nutricion (CIBERobn), Spain
| | - Daniel de Luis
- Center of Investigation of Endocrinology and Nutrition, Medicine School and Department of Endocrinology and Investigation, Hospital Clinico Universitario, University of Valladolid, Valladolid, Spain
| | - Felipe F Casanueva
- Molecular and Cellular Endocrinology Group. Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS) and Santiago de Compostela University (USC), Spain; CIBER Fisiopatologia de La Obesidad y Nutricion (CIBERobn), Spain
| |
Collapse
|
8
|
Abstract
Obesity is associated with an increased risk of various diseases and mortality. Although nearly 50 % of adults have been reported trying to lose weight, the prevalence of obesity has increased. One factor that hinders weight loss-induced decrease in obesity prevalence is weight regain. Although behavioural, psychological and physiological factors associated with weight regain have been reviewed, the information regarding the relationship between weight regain and genetics has not been previously summarised. In this paper, we comprehensively review the association between genetic polymorphisms and weight regain in adults and children with obesity after weight loss. Based on this information, identification of genetic polymorphism in patients who undergo weight loss intervention might be used to estimate their risks of weight regain. Additionally, the genetic-based risk estimation may be used as a guide for physicians and dietitians to provide each of their patients with the most appropriate strategies for weight loss and weight maintenance.
Collapse
|
9
|
Lorenzo PM, Izquierdo AG, Diaz-Lagares A, Carreira MC, Macias-Gonzalez M, Sandoval J, Cueva J, Lopez-Lopez R, Casanueva FF, Crujeiras AB. ZNF577 Methylation Levels in Leukocytes From Women With Breast Cancer Is Modulated by Adiposity, Menopausal State, and the Mediterranean Diet. Front Endocrinol (Lausanne) 2020; 11:245. [PMID: 32390948 PMCID: PMC7191069 DOI: 10.3389/fendo.2020.00245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022] Open
Abstract
The methylation levels of ZNF577 in breast tumors has been previously identified as a possible epigenetic mark of breast cancer associated with obesity. The aim of the current study was to investigate differences in methylation levels of ZNF577 depending on obesity, menopausal state and dietary pattern in blood leukocytes, a non-invasive sample. The methylation levels of ZNF577 of two CpG sites (CpGs) located in promoter and island previously identified as differentially methylated according to adiposity and menopausal state by 450 k array (cg10635122, cg03562414) were evaluated by pyrosequencing in DNA from the blood leukocytes of breast cancer patients [n = 90; n = 64 (71.1%) overweight/obesity and n = 26 (28.9%) normal-weight] and paired tumor tissue biopsies (n = 8 breast cancer patients with obesity; n = 3/5 premenopausal/postmenopausal women). Differences in methylation levels were evaluated at each CpGs individually and at the mean of the two evaluated CpGs. Adherence to the Mediterranean diet was evaluated using the MEDAS-validated questionnaire, and the consumption of food groups of interest was also evaluated using the recommended intakes of the Sociedad Española de Nutricion Comunitaria. The methylation levels of ZNF577 were correlated between paired leukocytes and breast tumor biopsies (r = 0.62; p = 0.001). Moreover, higher methylation was found in leukocytes from patients with obesity (p = 0.002) and postmenopausal patients (p = 0.022) than patients with normal-weight or premenopausal, respectively. After adjusting for the body mass index and age, higher levels of ZNF577 methylation were also found in women with greater adherence to the Mediterranean diet (p = 0.017) or specific foods. Relevantly, the methylation levels of ZNF577 showed a good ability for fish consumption detection [area under the ROC curve (AUC) = 0.72; p = 0.016]. In conclusion, the association between methylation of ZNF577 and adiposity, menopausal state, and adherence to the Mediterranean diet can be detected in the blood leukocytes. The results guarantee the need of performing further studies in longer longitudinal cohorts in order to elucidate the role of ZNF577 methylation in the association between breast cancer, adiposity and dietary patterns.
Collapse
Affiliation(s)
- Paula M. Lorenzo
- Laboratory of Epigenomics in Endocrinology and Nutrition (EpiEndoNut), Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Andrea G. Izquierdo
- Laboratory of Epigenomics in Endocrinology and Nutrition (EpiEndoNut), Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenetics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- CIBER de Oncologia (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos C. Carreira
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
- Laboratory of Molecular and Cellular Endocrinology, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain
| | - Manuel Macias-Gonzalez
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, University of Malaga (IBIMA) and CIBEROBN, Málaga, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit and Epigenomics Core Facility, Health Research Institute La Fe, Valencia, Spain
| | - Juan Cueva
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Rafael Lopez-Lopez
- CIBER de Oncologia (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Felipe F. Casanueva
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
- Laboratory of Molecular and Cellular Endocrinology, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain
| | - Ana B. Crujeiras
- Laboratory of Epigenomics in Endocrinology and Nutrition (EpiEndoNut), Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
- CIBER de Fisiopatologia de la Obesidad y Nutricion (CIBEOBN), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Ana B. Crujeiras
| |
Collapse
|